Abstract: Infections with apicomplexan parasites are major causes of several parasitic diseases in human and animal. Unfortunately, the drug misuse has slowly led to the wide and serious drugs resistance in apicomplexan parasites, rendering serial drugs much less effective. Developing new and effective drugs against parasitic diseases has become extremely urgent. Many apicomplexans have an electron transport chain (ETC) superficially resembling that of the yeast Saccharomyces cerevisiae. The inherent difference between ETC pathways of the parasite and the host make it an appealing target for the development of novel drug. It has recently been demonstrated that an “alternative” or type Ⅱ NADH dehydrogenases (NDH2s) involved in ETC is completely lacking in host, NDH2s were proposed to be promising drug targets against apicomplexa. ETC pathways and NDH2s of apicomplexan parasites were reviewed.